diff --git a/libraries/AP_GyroFFT/AP_GyroFFT.cpp b/libraries/AP_GyroFFT/AP_GyroFFT.cpp
index 82ac4fd49c..638a1eecef 100644
--- a/libraries/AP_GyroFFT/AP_GyroFFT.cpp
+++ b/libraries/AP_GyroFFT/AP_GyroFFT.cpp
@@ -248,10 +248,21 @@ void AP_GyroFFT::init(uint16_t loop_rate_hz)
         return;
     }
 
-    const uint8_t harmonics = _ins->get_gyro_harmonic_notch_harmonics();
+    // check for harmonics across all harmonic notch filters
+    // note that we only allow one harmonic notch filter linked to the FFT code
+    uint8_t harmonics = 0;
+    uint8_t num_notches = 0;
+    for (uint8_t i=0; i<HAL_INS_NUM_HARMONIC_NOTCH_FILTERS; i++) {
+        if (_ins->get_gyro_harmonic_notch_tracking_mode(i) == HarmonicNotchDynamicMode::UpdateGyroFFT) {
+            harmonics = _ins->get_gyro_harmonic_notch_harmonics(i);
+            num_notches = _ins->get_num_gyro_dynamic_notches(i);
+            break;
+        }
+    }
+
     // count the number of active harmonics or dynamic notchs
     _tracked_peaks = constrain_int16(MAX(__builtin_popcount(harmonics),
-        _ins->get_num_gyro_dynamic_notches()), 1, FrequencyPeak::MAX_TRACKED_PEAKS);
+                                         num_notches), 1, FrequencyPeak::MAX_TRACKED_PEAKS);
 
     // calculate harmonic multiplier. this assumes the harmonics configured on the 
     // harmonic notch reflect the multiples of the fundamental harmonic that should be tracked